def add_parm(self, parm, name=None):
""" Add a parm to the list """
# Make sure this parm is not part of the list already
if isinstance(parm, string_types):
name = parm
if name in self._parm_names:
raise DuplicateParm('%s already in ParmList' % name)
try:
parm = load_file(name, structure=True)
except FormatNotFound:
raise ParmError('Could not determine file type of %s' % name)
if not isinstance(parm, Structure):
raise ParmError('Added parm must be Structure or a subclass')
elif not isinstance(parm, Structure):
raise ParmError('Added parm must be Structure or a subclass')
else:
name = name or str(parm)
if name in self._parm_names:
raise DuplicateParm('%s already in ParmList' % parm)
# Otherwise, add in the new parm's name
self._parm_names.append(name)
self._parm_instances.append(parm)
# A newly added topology file is the currently active parm
self.current_index = len(self._parm_instances) - 1
self.parm = parm
def add_parm(self, parm, name=None):
""" Add a parm to the list """
# Make sure this parm is not part of the list already
if isinstance(parm, string_types):
name = parm
if name in self._parm_names:
raise DuplicateParm('%s already in ParmList' % name)
try:
parm = load_file(name, structure=True)
except FormatNotFound:
raise ParmError('Could not determine file type of %s' % name)
if not isinstance(parm, Structure):
raise ParmError('Added parm must be Structure or a subclass')
elif not isinstance(parm, Structure):
raise ParmError('Added parm must be Structure or a subclass')
else:
name = name or str(parm)
if name in self._parm_names:
raise DuplicateParm('%s already in ParmList' % parm)
# Otherwise, add in the new parm's name
self._parm_names.append(name)
self._parm_instances.append(parm)
# A newly added topology file is the currently active parm
self.current_index = len(self._parm_instances) - 1
self.parm = parm
def __init__(self, fname, seq=None):
super(XyzFile, self).__init__()
if isinstance(fname, string_types):
fxyz = genopen(fname, 'r')
own_handle_xyz = True
else:
fxyz = fname
own_handle_xyz = False
if seq is not None:
seqstruct = load_file(seq)
# Now parse the file
try:
natom = int(fxyz.readline().split()[0])
except (ValueError, IndexError):
raise TinkerError('Bad XYZ file format; first line')
if seq is not None and natom != len(seqstruct.atoms):
raise ValueError(
'Sequence file %s # of atoms does not match the # '
'of atoms in the XYZ file' % seq)
words = fxyz.readline().split()
if len(words) == 6 and not XyzFile._check_atom_record(words):
self.box = [float(w) for w in words]
words = fxyz.readline().split()
atom = Atom(atomic_number=AtomicNum[element_by_name(words[1])],
name=words[1],
type=words[5])
atom.xx, atom.xy, atom.xz = [float(w) for w in words[2:5]]
residue = Residue('SYS')
residue.number = 1
residue._idx = 0
if seq is not None:
residue = seqstruct.residues[0]
self.add_atom(atom, residue.name, residue.number, residue.chain,
residue.insertion_code, residue.segid)
bond_ids = [[int(w) for w in words[6:]]]
for i, line in enumerate(fxyz):
words = line.split()
atom = Atom(atomic_number=AtomicNum[element_by_name(words[1])],
name=words[1],
type=words[5])
atom.xx, atom.xy, atom.xz = [float(w) for w in words[2:5]]
if seq is not None:
residue = seqstruct.atoms[i + 1].residue
self.add_atom(atom, residue.name, residue.number, residue.chain,
residue.insertion_code, residue.segid)
bond_ids.append([int(w) for w in words[6:]])
# All of the bonds are stored now -- go ahead and make them now
for atom, bonds in zip(self.atoms, bond_ids):
i = atom.idx + 1
for idx in bonds:
if idx > i:
self.bonds.append(Bond(atom, self.atoms[idx - 1]))
if own_handle_xyz:
fxyz.close()
def _amber_to_gromacs(self):
# Load prmtop and inpcrd as a Structure
parmstruct = load_file(self.outprefix + ".prmtop",
xyz=self.outprefix + ".inpcrd",
structure=True)
# Save .gro coordinate file
GromacsGroFile.write(struct=parmstruct, dest=self.outprefix + ".gro")
# Save .top topology and parameter file
grotop = GromacsTopologyFile.from_structure(parmstruct, copy=False)
grotop.write(dest=self.outprefix + ".top", parameters="inline")
def __init__(self, fname, seq=None):
super(XyzFile, self).__init__()
if isinstance(fname, string_types):
fxyz = genopen(fname, 'r')
own_handle_xyz = True
else:
fxyz = fname
own_handle_xyz = False
if seq is not None:
seqstruct = load_file(seq)
# Now parse the file
try:
natom = int(fxyz.readline().split()[0])
except (ValueError, IndexError):
raise TinkerError('Bad XYZ file format; first line')
if seq is not None and natom != len(seqstruct.atoms):
raise ValueError('Sequence file %s # of atoms does not match the # '
'of atoms in the XYZ file' % seq)
words = fxyz.readline().split()
if len(words) == 6 and not XyzFile._check_atom_record(words):
self.box = [float(w) for w in words]
words = fxyz.readline().split()
atom = Atom(atomic_number=AtomicNum[element_by_name(words[1])],
name=words[1], type=words[5])
atom.xx, atom.xy, atom.xz = [float(w) for w in words[2:5]]
residue = Residue('SYS')
residue.number = 1
residue._idx = 0
if seq is not None:
residue = seqstruct.residues[0]
self.add_atom(atom, residue.name, residue.number, residue.chain,
residue.insertion_code, residue.segid)
bond_ids = [[int(w) for w in words[6:]]]
for i, line in enumerate(fxyz):
words = line.split()
atom = Atom(atomic_number=AtomicNum[element_by_name(words[1])],
name=words[1], type=words[5])
atom.xx, atom.xy, atom.xz = [float(w) for w in words[2:5]]
if seq is not None:
residue = seqstruct.atoms[i+1].residue
self.add_atom(atom, residue.name, residue.number, residue.chain,
residue.insertion_code, residue.segid)
bond_ids.append([int(w) for w in words[6:]])
# All of the bonds are stored now -- go ahead and make them now
for atom, bonds in zip(self.atoms, bond_ids):
i = atom.idx + 1
for idx in bonds:
if idx > i:
self.bonds.append(Bond(atom, self.atoms[idx-1]))
if own_handle_xyz:
fxyz.close()
def _prmtop_to_charmm(self):
"""
Converts an AMBER prmtop with AMBER parameters to a psf file,
using ParmEd.
"""
# Save PSF topology and parameter file
parmstruct = load_file(self.outprefix + ".prmtop",
xyz=self.outprefix + ".inpcrd",
structure=True)
parmstruct.save(self.outprefix + ".psf", format="psf")
# Save PDB file with coordinates
m = molecule.load("parm7", self.outprefix + ".prmtop", "rst7",
self.outprefix + ".inpcrd")
atomsel("all", m).write("pdb", self.outprefix + ".pdb")
molecule.delete(m)
def test_gromacs_amber(tmpdir):
from dabble.param import GromacsWriter
p = str(tmpdir)
molid = molecule.load("mae", os.path.join(dir, "prepped.mae"))
w = GromacsWriter(molid,
tmp_dir=p,
forcefield="amber",
extra_topos=[
os.path.join(dir, "glx.off"),
os.path.join(dir, "lyx.off")
],
extra_params=[
os.path.join(dir, "join.frcmod"),
os.path.join(dir, "analogies.frcmod")
],
override_defaults=False)
w.write(os.path.join(p, "test"))
# Load and check the output file
m2 = molecule.load("gro", os.path.join(p, "test.gro"))
molecule.set_top(m2)
# Check the two custom residues are present
assert len(atomsel("resname GLX")) == 7
assert len(atomsel("resname LYX")) == 20
# Check that the isopeptide bond is there
lybonds = []
for x in atomsel("resname LYX").bonds:
lybonds.extend(x)
assert any(x in lybonds for x in atomsel("resname GLX").index)
# Check the parameterized file with parmed API
from parmed.formats.registry import load_file
f = load_file(os.path.join(p, "test.top"))
assert f.residues[153].name == "GLX"
assert "n2" in [_.type for _ in f.residues[153].atoms]
assert "n2" not in [_.type for _ in f.residues[152].atoms]
assert "N" in [_.type for _ in f.residues[152].atoms]
